Automated Design\nof Oligopools and Rapid Analysis\nof Massively Parallel Barcoded Measurements

Oligopool synthesis\nand next-generation sequencing enable the construction\nand characterization of large libraries of designed genetic parts\nand systems. As library sizes grow, it becomes computationally challenging\nto optimally design large numbers of primer binding sites, barcode\nsequences, and overlap regions to obtain efficient assemblies and\nprecise measurements. We present the Oligopool Calculator, an end-to-end\nsuite of algorithms and data structures that rapidly designs many\nthousands of oligonucleotides within an oligopool and rapidly analyzes\nmany billions of barcoded sequencing reads. We introduce several novel\nconcepts that greatly increase the design and analysis throughput,\nincluding orthogonally symmetric barcode design, adaptive decision\ntrees for primer design, a Scry barcode classifier, and efficient\nread packing. We demonstrate the Oligopool Calculator’s capabilities\nacross computational benchmarks and real-data projects, including\nthe design of over four million highly unique and compact barcodes\nin 1.2 h, the design of universal primer binding sites for one million\n200-mer oligos in 15 min, and the analysis of about 500 million deep\nsequencing reads per hour, all on an 8-core desktop computer. Overall,\nthe Oligopool Calculator accelerates the creative use of massively\nparallel experiments by eliminating the computational complexity of\ntheir design and analysis.